Hi Panos, The motion correction itself is carried out using the mri_robust_template binary. The motion correction step also includes an mri_convert command to conform the volume and mri_add_xform_to_header.
example taken from recon-all dev table: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
mri_robust_template --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout --subsample 200 --lta
-Louis
On Mon, 15 Jul 2013, Fotiadis, Panagiotis wrote:
Hi FS Community,
I was wondering which command(s) is(are) being used in the "Motion Correction" part of the recon-all process, to merge the mri/orig/XXX.mgz files and correct for any motion. Thank you for your time!
Best, Panos _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer